The overall objective of the proposed research is to identify and map networks of gene interactions in Saccharomyces cerevisiae. The strategy is to identify genes whose mRNA abundance is altered as a consequence of directed gene perturbations; initially, these will be single-gene replacements. The basic method to be used is the hybridization of cDNAs derived from wild-type and experimental strains to arrays of all known and predicted yeast genes. The hybridization signals will be quantified to obtain values of relative gene expression among the different experimental samples. As a model system, we will analyze gene interactions in a complex, poorly understood, interorganelle communication network called the retrograde response, in which changes in the functional state of mitochondria result in changes in expression of a large but unidentified subset of nuclear genes. Four specific aims are proposed: 1) to construct a high throughput microdisplay system, patterned after an existing design, for the analysis of expression of all known and predicted yeast genes; 2) to identify genes and pathways that constitute the retrograde response; 3) to develop general methodology for the identification, analysis and presentation of networks of gene interactions; and 4) to make the technology, reagents and data available to the scientific community. The general methodology will involve tabulation and graphical analysis of the data to obtain, as a long range goal, i) the relative expression value of any given gene in the yeast genome as it samples all viable single-gene replacements, and, as a short term goal, ii) an array of genes organized as nested sets whose expression changes in response to a given single-gene replacement, beginning with known genes in the retrograde response pathways. These studies are aimed at furthering our understanding of polygenic interactions that underlie poorly understood genetic phenomena such as penetrance and quantitative traits.